TOLEDO, Ohio (CNN) -- Sen. John McCain on Thursday denied assertions published in The New York Times that he once had a close relationship with a female lobbyist whose clients had business before his Senate committee.

Sen. John McCain, with his wife, Cindy, at his side, said The New York Times report is "not true."

"I'm disappointed in The New York Times piece. It's not true," he told reporters in Toledo, Ohio, his wife, Cindy, standing by his side.

He added that he has never "done anything that would betray the public trust or make a decision" that would favor a particular group.

His wife added that her husband always puts family and country first, and is "a man of great character."

"We publish stories when they are ready," Executive Editor Bill Keller said in a statement, explaining that the story reached his desk Tuesday. " 'Ready' means the facts have been nailed down to our satisfaction, the subjects have all been given a full and fair chance to respond and the reporting has been written up with all the proper context and caveats.

"This story was no exception. It was a long time in the works."

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The newspaper reported in its online edition Wednesday that aides to McCain's 2000 presidential campaign were so worried about the relationship that they confronted McCain and the lobbyist, Vicki Iseman.

Also, some McCain advisers were concerned that the relationship had become romantic, The New York Times reported.

"A former campaign adviser described being instructed to keep Ms. Iseman away from the senator at public events, while a Senate aide recalled plans to limit Ms. Iseman's access to his offices," the paper reported.

The paper's assertions were part of a larger article on McCain's relationships with and stances toward lobbyists and special interests.

The Arizona senator has dominated the Republican primaries, handily pulling away from former Arkansas Gov. Mike Huckabee in the race for the GOP presidential nomination.

Huckabee stayed out of the crossfire Thursday, saying only that McCain is "a good and decent and honorable man."

"Today he denied that any of that was true, I take him at his word," Huckabee said on the campaign trail in Houston, Texas.

McCain said in a news conference Thursday that he never had discussions with any staffers about an inappropriate relationship with Iseman. He also denied having a romantic relationship with her. If staffers had such concerns, McCain told reporters, they never conveyed them to him.

The New York Times quoted what it said were two admittedly "disillusioned" former McCain associates who said they approached the senator and the lobbyist about their concerns. "Both said Mr. McCain acknowledged behaving inappropriately," the newspaper reported.

McCain further described his relationship with Iseman as a friendship and said he had "seen her on occasion, particularly at receptions and fundraisers and appearances before the committee." Asked if he was closer to Iseman than he was other lobbyists, McCain flatly said no.

McCain's former top political adviser, John Weaver, told the newspaper that he met with Iseman at Washington's Union Station during McCain's first presidential bid. He asked her to stay away from the senator, the paper reported, because McCain was running on a platform of political reform and shunning special interests.

Iseman represented telecommunications companies with business before the Senate Commerce Committee that McCain led, according to the newspaper.

"Ms. Iseman's involvement in the campaign, it was felt by us, could undermine that effort," Weaver told the Times.

In a Thursday interview with CNN, Weaver said he approached Iseman because she was telling people she had special access to and influence with McCain.

The New York Times story does not claim Weaver and Iseman discussed any romantic relationship, and Weaver told CNN they never talked about it because "there was no reason to."

"My concern wasn't about anything John had done; it was about her comments. It was about access she claimed to have had," Weaver told CNN.

Weaver left the McCain camp in summer 2007, but he said he still talks to the senator's campaign officials daily.

Iseman acknowledged the Union Station meeting but disputed Weaver's account, according to The New York Times.

"I never discussed with him alleged things I had 'told people,' that had made their way 'back to' him," Iseman told the newspaper in an e-mail. She added that she never received special treatment from McCain's office, according to the paper.

As for claims that McCain's advisers were concerned about a possible romantic relationship, Iseman told the newspaper the claims were unfounded.

Iseman works for the consulting firm Alcalde & Fay. Among its clients are several large telecommunications firms.

The firm said in a Thursday statement that The New York Times story -- based on "malicious innuendo" -- was "completely and utterly false." It added that the firm's relationship with McCain was "professional" and "appropriate."

"The story is based upon the fantasies of a disgruntled former campaign employee and is without foundation or merit," the statement said. "It is beneath the dignity of a quality newspaper to participate in such a campaign of character assassination."

Attempts to reach Iseman were unsuccessful, but the Alcalde & Fay statement said she enjoys the firm's support.

In his Thursday news conference, McCain called Weaver "a friend." Of the alleged Union Station meeting, he said, "I don't know anything about it."

"Since it was in The New York Times, I don't take it at face value," he said.

Hours after the newspaper posted its story, McCain's advisers challenged the accuracy of the Times' article and questioned the newspaper's motivation.

Campaign spokeswoman Jill Hazelbaker said in a statement that the newspaper had engaged in a "smear campaign" and that nothing in the story suggests "that John McCain ever violated the principles that have guided his career."

One of McCain's senior advisers, Charlie Black, told CNN that the campaign first learned in October the paper was working on a story about McCain's relationship with Iseman. Watch Black address the allegations »

He said that information and documents provided to the paper disputes suggestions McCain tried to use his influence to help Iseman.

Black further said The New York Times was a liberal newspaper that was printing "rumors and gossip" in what he described as a partisan attack on the conservative McCain.

"He doesn't do favors for anyone," Black said of McCain.

Despite the attacks launched on the newspaper from the McCain camp, William Bennett, a conservative commentator who contributes to CNN, said The New York Times may have helped the McCain campaign.

"The New York Times may have done for John McCain what John McCain did not, up to this point, do for himself, which is bring a lot of conservatives in," Bennett said. E-mail to a friend